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This page was generated on 2023-11-02 11:41:21 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2094/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
synergyfinder 3.10.0  (landing page)
Shuyu Zheng
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/synergyfinder
git_branch: RELEASE_3_18
git_last_commit: 12875aa
git_last_commit_date: 2023-10-24 10:52:43 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for synergyfinder on kunpeng2


To the developers/maintainers of the synergyfinder package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/synergyfinder.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: synergyfinder
Version: 3.10.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:synergyfinder.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings synergyfinder_3.10.0.tar.gz
StartedAt: 2023-11-02 14:46:30 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 14:48:27 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 117.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: synergyfinder.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:synergyfinder.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings synergyfinder_3.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/synergyfinder.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘synergyfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘synergyfinder’ version ‘3.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘synergyfinder’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘scales’
Namespaces in Imports field not imported from:
  ‘future’ ‘gstat’ ‘nleqslv’ ‘sp’ ‘tidyverse’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.Extract2DrugPlotData: no visible binding for global variable
  ‘input_type’
.Extract2DrugPlotData: no visible binding for global variable
  ‘block_id’
.Extract2DrugPlotData: no visible binding for global variable ‘value’
.Extract2DrugPlotData: no visible binding for global variable ‘left’
.Extract2DrugPlotData: no visible binding for global variable ‘right’
.Extract2DrugPlotData: no visible binding for global variable ‘conc1’
.Extract2DrugPlotData: no visible binding for global variable ‘conc2’
.Extract2DrugPlotData: no visible binding for global variable ‘text’
.ExtractMultiDrugPlotData: no visible binding for global variable
  ‘block_id’
Bliss: no visible binding for global variable ‘Bliss_ref’
CalculateCSS: no visible binding for global variable ‘data’
CalculateSensitivity: no visible binding for global variable
  ‘response_origin’
CalculateSensitivity: no visible binding for global variable ‘block_id’
CalculateSynergy: no visible binding for global variable
  ‘response_origin’
CalculateSynergy: no visible binding for global variable ‘block_id’
CalculateSynergy: no visible global function definition for ‘t.test’
HSA: no visible binding for global variable ‘HSA_ref’
HighlightBarPlot: no visible binding for global variable ‘id’
HighlightBarPlot: no visible binding for global variable ‘value’
HighlightBarPlot: no visible binding for global variable ‘color’
Plot2DrugHeatmap: no visible binding for global variable ‘text’
PlotBarometer: no visible binding for global variable ‘block_id’
PlotBarometer: no visible binding for global variable ‘response_mean’
PlotBarometer: no visible binding for global variable ‘response’
PlotBarometer: no visible binding for global variable ‘r’
PlotBarometer: no visible binding for global variable ‘theta’
PlotBarometer: no visible binding for global variable ‘value’
PlotBarometer: no visible binding for global variable ‘start’
PlotBarometer: no visible binding for global variable ‘end’
PlotBarometer: no visible binding for global variable ‘label’
PlotBarometer: no visible binding for global variable ‘x’
PlotBarometer: no visible binding for global variable ‘y’
PlotBarometer: no visible binding for global variable ‘adjust’
PlotBarometer: no visible binding for global variable ‘angle’
PlotDoseResponseCurve: no visible binding for global variable
  ‘response_origin’
PlotDoseResponseCurve: no visible binding for global variable
  ‘block_id’
PlotDoseResponseCurve: no visible global function definition for
  ‘dev.list’
PlotDoseResponseCurve: no visible global function definition for
  ‘dev.off’
PlotMultiDrugBar: no visible binding for global variable ‘id’
PlotMultiDrugBar: no visible binding for global variable ‘value’
PlotMultiDrugBar: no visible binding for global variable ‘color’
PlotMultiDrugBar: no visible binding for global variable ‘metric’
PlotSensitivitySynergy: no visible binding for global variable
  ‘block_id’
PlotSensitivitySynergy: no visible binding for global variable ‘css’
PlotSensitivitySynergy: no visible binding for global variable ‘label’
PlotSensitivitySynergy: no visible binding for global variable
  ‘synergy’
ReshapeData: no visible binding for global variable ‘block_id’
ReshapeData: no visible binding for global variable ‘n’
ReshapeData: no visible global function definition for ‘head’
ReshapeData: no visible binding for global variable ‘response_origin’
ReshapeData: no visible binding for global variable ‘nn’
ReshapeData: no visible binding for global variable ‘maxn’
ReshapeData: no visible binding for global variable ‘response_sd’
ReshapeData: no visible binding for global variable ‘response_sem’
ReshapeData: no visible binding for global variable ‘response_mean’
ReshapeData: no visible binding for global variable ‘response_CI95’
ReshapeData: no visible binding for global variable
  ‘response_origin_sd’
ReshapeData: no visible binding for global variable
  ‘response_origin_sem’
ReshapeData: no visible binding for global variable
  ‘response_origin_mean’
ReshapeData: no visible binding for global variable
  ‘response_origin_CI95’
ZIP : <anonymous>: no visible binding for global variable ‘data’
ZIP : <anonymous>: no visible binding for global variable ‘pred’
ZIP : <anonymous>: no visible global function definition for ‘:=’
ZIP: no visible binding for global variable ‘.’
ZIP: no visible binding for global variable ‘ZIP_fit’
ZIP: no visible binding for global variable ‘ZIP_ref’
ZIP: no visible binding for global variable ‘ZIP_synergy’
Undefined global functions or variables:
  . := Bliss_ref HSA_ref ZIP_fit ZIP_ref ZIP_synergy adjust angle
  block_id color conc1 conc2 css data dev.list dev.off end head id
  input_type label left maxn metric n nn pred r response response_CI95
  response_mean response_origin response_origin_CI95
  response_origin_mean response_origin_sd response_origin_sem
  response_sd response_sem right start synergy t.test text theta value
  x y
Consider adding
  importFrom("grDevices", "dev.list", "dev.off")
  importFrom("graphics", "text")
  importFrom("stats", "end", "start", "t.test")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) FitDoseResponse.Rd:55: Escaped LaTeX specials: \&
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
CalculateSensitivity 30.164  0.283  30.508
PlotMultiDrugSurface 19.460  0.176  19.663
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/synergyfinder.Rcheck/00check.log’
for details.



Installation output

synergyfinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL synergyfinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘synergyfinder’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (synergyfinder)

Tests output


Example timings

synergyfinder.Rcheck/synergyfinder-Ex.timings

nameusersystemelapsed
Bliss0.3000.0000.301
CalculateRI1.5090.1281.640
CalculateSensitivity30.164 0.28330.508
CalculateSynergy1.9400.0241.968
CorrectBaseLine0.2310.0000.231
ExtractSingleDrug0.1580.0080.165
FindModelType0.0180.0000.019
FitDoseResponse0.0190.0000.019
HSA0.1730.0000.174
Loewe0.3490.0000.350
Plot2DrugContour1.5970.0161.622
Plot2DrugHeatmap0.4660.0030.470
Plot2DrugSurface0.7500.0240.776
PlotBarometer2.5950.0162.616
PlotDoseResponse000
PlotDoseResponseCurve0.2480.0040.252
PlotMultiDrugBar3.6210.0283.656
PlotMultiDrugSurface19.460 0.17619.663
PlotSensitivitySynergy4.0090.0324.049
PlotSynergy2.0880.0042.097
ReshapeData0.1630.0000.164
ZIP0.7580.0000.759